Since the inexact user-transformer relation in low-voltage area network influences the business development of loss management, three-phase unbalanced management, breakdown rescue, etc. severely, and the current identification method cannot consider both the accuracy and power distribution reliability, a user-transformer relation identification method based on characteristic current is proposed in this paper. In this method, the load resistance switching is applied to generate the harmonic current, the sliding discrete fourier transform (DFT) is adopted to extract and decode in real time, then the user-transformer relation is obtained through the comparison with target code bits, and the phase affiliation is determined by the comparison among three phase current magnitude. The results of field pilot show that the proposed method in this paper can identify the user-transformer relation accurately, and has good application effect and popularization value.